Evolutionary dynamics of piRNA clusters in Drosophila

Evolution of genome structure in the Drosophila simulans species complex

(2021) Mahul Chakraborty et al.   GENOME RESEARCH

Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation

(2021) Daniel Gebert et al.   MOLECULAR CELL

Transposon-taming piRNAs in the germline: Where do they come from?

(2021) Peiwei Chen et al.   MOLECULAR CELL

piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

(2020) Robert Kofler   Genome Biology and Evolution

Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations

(2020) Shuo Zhang et al.   GENOME RESEARCH

Transposable elements in individual genotypes of Drosophila simulans

(2020) Sarah Signor   Ecology and Evolution

Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century

(2020) Florian Schwarz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamics of Transposable Element Invasions with piRNA Clusters

(2019) Robert Kofler   MOLECULAR BIOLOGY AND EVOLUTION

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Molecular dissection of a natural transposable element invasion

(2018) Robert Kofler et al.   GENOME RESEARCH

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element

(2018) Erin S Kelleher et al.   Genome Biology and Evolution

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants

(2017) Sarah A Signor et al.   Genome Biology and Evolution

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

(2017) Jeffrey R. Adrion et al.   Genome Biology and Evolution

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

Conservation of social effects (Ψ) between two species of Drosophila despite reversal of sexual dimorphism

(2017) Sarah A. Signor et al.   Ecology and Evolution

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

Tempo and Mode of Transposable Element Activity in Drosophila

(2015) Robert Kofler et al.   PLoS Genetics

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

(2015) Gung-wei Chirn et al.   PLoS Genetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing

(2014) Adrien Le Thomas et al.   GENES & DEVELOPMENT

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

A Transgenerational Process Defines piRNA Biogenesis in Drosophila virilis

(2014) Adrien Le Thomas et al.   Cell Reports

Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline

(2014) Sergey Shpiz et al.   PLoS Genetics

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

(2014) Lidia Mateo et al.   PLoS Genetics

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment

(2013) Ivan Olovnikov et al.   NUCLEIC ACIDS RESEARCH

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

(2013) V. Zanni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity

(2013) Nicole Darricarrère et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements on Drosophila

(2012) Yuh Chwen G. Lee et al.   GENETICS

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

(2012) E. G. King et al.   GENOME RESEARCH

A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans

(2012) Cristina Vieira et al.   JOURNAL OF ENVIRONMENTAL RADIOACTIVITY

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

(2012) Darren J. Obbard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes

(2010) Emmanuelle Lerat et al.   GENE

Transposable elements in natural populations of Drosophila melanogaster

(2010) Y. C. G. Lee et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary dynamics of transposable elements in a small RNA world

(2010) Justin P. Blumenstiel   TRENDS IN GENETICS

Multiple Roles for Heterochromatin Protein 1 Genes in Drosophila

(2009) Danielle Vermaak et al.   Annual Review of Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

(2009) J. Lu et al.   GENOME RESEARCH

Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

(2009) R. Assis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY